Cancer risk biomarker

• US 8,765,368 B2
• Filed: 09/17/2008
• Issued: 07/01/2014
• Est. Priority Date: 09/17/2007
• Status: Active Grant

• Current Assignee: University of Toledo
• Original Assignee: University of Toledo
• Inventors: Willey, James C., Blomquist, Thomas M., Crawford, Erin L., Mullins, D'Anna N.
• Primary Examiner(s): SWITZER, JULIET CAROLINE
• Application Number:
  US12/212,003
• Publication Number:
  US 20090181383A1
• Time in Patent Office: 2,113 Days
• Field of Search: None
• US Class Current: 435/6.1
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2545/114 involving a quantitation step
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• CPC Class Codes: G01N 2800/50 Determining the risk of developing a disease
• CPC Class Codes: G01N 33/574 for cancer

Abstract

The present disclosure relates to methods and compositions for identifying biomarkers that indicate a biological state, in particular cancer or predisposition to cancer. Also provided are methods and compositions for identifying a greater risk for a cancer-related condition in an subject.

Claims

1. A method of identifying a greater risk for developing bronchogenic carcinoma in a human subject comprising:

(a) assaying a bronchial epithelial cell sample from the subject;

(b) determining transcript abundance (TA) for a group of genes in the sample;

wherein TA levels are determined by microarray analysis, quantitative polymerase chain reaction, or a combination of both for 7 or more genes selected from the group of genes consisting of;

CEBPG, E2F1, E2F6, XRCC1, ERCC4, ERCC5, GPX1, GPX3, GSTM3, GSTP1, GSTT1, GSTZ1, MGST1, SOD1 and CAT;

(c) comparing the TAs of step (b) to threshold levels for each gene, wherein the threshold levels comprise (molecules/10⁶ β

-actin);

2. The method of claim 1, wherein the step (b) of determining transcript abundance includes assaying transcript abundance by:

i) measuring a nucleic acid corresponding to each gene of the 7 or more genes selected from the group of genes relative to its competitive template;

ii) co-measuring a nucleic acid corresponding to a housekeeping gene with its competitive template; and

iii) obtaining a relation comparing values obtained from the co-measurements obtained from steps i) and ii).

3. The method of claim 2, wherein the nucleic acid for each gene refers to an mRNA transcript of the gene or a cDNA obtained from the mRNA.

4. The method of claim 2, wherein the relation obtained can be a comparison of values for each gene, its competitive template, the housekeeping gene, and its competitive template.

5. The method of claim 2, wherein each gene is measured relative to a reference nucleic acid.

6. A method for selecting a therapy for a subject having a greater risk for developing bronchogenic carcinoma, comprising:

(a) assaying a bronchial epithelial cell sample from the subject;

(b) determining transcript abundance (TA) levels for a group of genes in the sample, wherein TA levels are determined by microarray analysis, quantitative polymerase chain reaction, or a combination of both for 7 or more genes selected from the group of genes consisting of;

CEBPG, E2F1, E2F6, XRCC1, ERCC4, ERCC5, GPX1, GPX3, GSTM3, GSTP1, GSTT1, GSTZ1, MGST1, SOD1 and CAT;

(c) comparing the TA levels of step (b) to threshold levels for each gene, wherein the threshold levels comprise (molecules/10⁶ β

-actin);